Still short on time; won’t address the “hour instead of 48-52 minutes” change except to note that it depends – some early timetables I used for graphs had travel times of 57 minutes from Northwest to downtown already, in other words. Instead, let’s address the other big change.
From Ben Wear’s article, note the following quotes:

Foregoing the Leander and Lakeline stops on some morning and afternoon trips, officials said, might be necessary partly to ensure that passengers from those two stops don’t fill all the trains and preclude boardings at closer-in Austin stops.

Also Wednesday, Capital Metro officials also said they now plan to use only four of the six trains, which the agency purchased for about $6 million each, because the line has just four limited sections where there is dual track to allow northbound and southbound trains to pass one another.
“We’ve found that it could be operated best with four trains,” spokesman Adam Shaivitz said, rather than the five that the agency had said previously would typically be in service. The other two would be held in reserve and used in case of breakdowns.

So, here’s a little thought experiment. Suppose you honestly believe that demand for your new rail service is going to be really, really high – so high that, as they put it, full trains from further up the line will prevent people from even boarding closer in.
What do you do to solve this problem? Do you:
1. Run with the originally planned 5 trains (out of the 6 you ‘leased’)
2. Increase service to run with all 6 trains while you arrange for another couple to be built and shipped
3. Cut service to run with only 4 trains

1. Fare Enough, local blog by Larry Schooler, covering some Austin transit and has some experience with Tri-Rail. Welcome.
2. Cap Metro has come out with their service recommendations for 2020 and they’re awful – just off the top of my head, running the #5 on San Jacinto because Guadalupe is “too congested” (hint: it’s congested because that’s where all the good stuff people actually want to go to is located); completely eliminating 3 superior express bus routes in favor of the objectively inferior Red Line + shuttle-bus solution, destroying the utility of the #21/#22 for the schoolkids; etc.
The usual narrative with light rail, which I find to be inaccurate, is that forcing bus riders to transfer to light rail is a degradation of their service. IE, people in Houston in the pocket of the anti-rail lobby stirred up bus riders with objectively false claims that their service would be degraded – when it would actually be improved (shorter ride in traffic on bus with new congestion-skipping ride on rail, no change to endpoint of service). The problem in our case isn’t that we’re making people transfer from bus to rail, it’s actually that we’re making people transfer from congestion-skipping rail to traffic-snarled bus at the work end of the trip, which as South Florida has conclusively shown with Tri-Rail, is the kiss of death among ‘choice commuters’. People with real jobs don’t want to have to worry about whether their shuttle bus back to the train station will make it or whether they’ll have to wait a half-hour for the next train; they want to be walking from the train station to their office and back again, period.
More on this tomorrow I hope.